module 2: lecture 1 enzymes in genetic engineering

NPTEL – Bio Technology – Genetic Engineering & Applications

Joint initiative of IITs and IISc – Funded by MHRD of 30

MODULE 2: LECTURE 1

ENZYMES IN GENETIC ENGINEERING: RESTRICTION

NUCLEASES: EXO & ENDO NUCLEASES

2-1.1 Introduction: A restriction enzyme is a nuclease enzyme that cleaves DNA sequence at a

random or specific recognition sites known as restriction sites. In bacteria, restriction

enzymes form a combined system (restriction + modification system) with modification

enzymes that methylate the bacterial DNA. Methylation of bacterial DNA at the

recognition sequence typically protects the own DNA of the bacteria from being cleaved

by restriction enzyme.

There are two different kinds of restriction enzymes:

(1) Exonucleases catalyses hydrolysis of terminal nucleotides from the end of DNA or

RNA molecule either 5’to 3’ direction or 3’ to 5’ direction. Example: exonuclease I,

exonuclease II etc.

(2) Endonucleases can recognize specific base sequence (restriction site) within DNA or

RNA molecule and cleave internal phosphodiester bonds within a DNA molecule.

Example: EcoRI, Hind III, BamHI etc.

2-1.2History: In 1970 the first restriction endonuclease enzyme HindII was isolated. For the

subsequent discovery and characterization of numerous restriction endonucleases, in

1978 Daniel Nathans, Werner Arber, and Hamilton O. Smith awarded for Nobel Prize for

Physiology or Medicine. Since then, restriction enzymes have been used as an essential

tool in recombinant DNA technology.



2-1.3 Restriction Endonuclease Nomenclature: Restriction endonucleases are named according to the organism in which they

were discovered, using a system of letters and numbers. For example, HindIII

(pronounced “hindee-three”) was discovered in Haemophilus influenza (strain d). The

Roman numerals are used to identify specific enzymes from bacteria that contain multiple

restriction enzymes indicating the order in which restriction enzymes were discovered in

a particular strain.

2-1.4 Classification of Restriction Endonucleases: There are three major classes of restriction endonucleases based on the types of

sequences recognized, the nature of the cut made in the DNA, and the enzyme structure:

• Type I restriction enzymes

• Type II restriction enzymes

• Type III restriction enzymes

2-1.4.1 Type I restriction enzymes:

• These enzymes have both restriction and modification activities. Restriction

depends upon the methylation status of the target DNA.

• Cleavage occurs approximately 1000 bp away from the recognition site.

• The recognition site is asymmetrical and is composed of two specific portions in

which one portion contain 3–4 nucleotides while another portion contain 4–5



nucleotides and both the parts are separated by a non-specific spacer of about 6–8

nucleotides.

• They require S-adenosylmethionine (SAM), ATP, and magnesium ions (Mg2+)

for activity.

• These enzymes are composed of mainly three subunits, a specificity subunit that

determines the DNA recognition site, a restriction subunit, and a modification

subunit

2-1.4.2 Type II restriction enzymes:

• Restriction and modification are mediated by separate enzymes so it is possible to

cleave DNA in the absence of modification. Although the two enzymes recognize

the same target sequence, they can be purified separately from each other.

• Cleavage of nucleotide sequence occurs at the restriction site.

• These enzymes are used to recognize rotationally symmetrical sequence which is

often referred as palindromic sequence.

• These palindromic binding site may either be interrupted (e.g. BstEII recognizes

the sequence 5´-GGTNACC-3´, where N can be any nucleotide) or continuous

(e.g. KpnI recognizes the sequence 5´-GGTACC-3´).

• They require only Mg2+ as a cofactor and ATP is not needed for their activity.

• Type II endonucleases are widely used for mapping and reconstructing DNA in

vitro because they recognize specific sites and cleave just at these sites.

The steps involved in DNA binding and cleavage by a type II restriction

endonuclease:

• These enzymes have nonspecific contact with DNA and initially bind to DNA as

dimmers.

• The target site is then located by a combination of linear diffusion or “sliding” of

the enzyme along the DNA over short distances, and hopping/jumping over

longer distances.



• Once the target restriction site is located, the recognition process (coupling)

triggers large conformational changes of the enzyme and the DNA, which leads to

activation of the catalytic center.

• Catalysis results in hydrolysis of phosphodiester bond and product release.

Fig 2-1.4.2: Structures of free, nonspecific, and specific DNA-bound forms of BamHI.

The two dimers are shown in brown, the DNA backbone is in green and the bases in gray.

BamHI becomes progressively more closed around the DNA as it goes from the

nonspecific to specific DNA binding mode.



2-1.4.3 Type III restriction enzymes:

• These enzymes recognize and methylate the same DNA sequence but

cleave 24–26 bp away.

• They have two different subunits, in which one subunit (M) is responsible

for recognition and modification of DNA sequence and other subunit (R)

has nuclease action.

• Mg+2 ions, ATP are needed for DNA cleavage and process of cleavage is

stimulated by SAM.

• Cleave only one strand. Two recognition sites in opposite orientation are

necessary to break the DNA duplex.

Property Type I RE Type II RE Type III RE

Abundance Less common than

Type II

Most common Rare

Recognition site Cut both strands at a

nonspecific

location > 1000 bp

away from

recognition site

Cut both strands at

a specific, usually

palindromic

recognition site (4-8

bp)

Cleavage of one

strand, only 24-26

bp downstream of

the 3´ recognition

site

Restriction and

modification

Single

multifunctional

enzyme

Separate nuclease

and methylase

Separate enzymes

sharing a

common subunit

Nuclease subunit

structure

Heterotrimer Homodimer Heterodimer

Cofactors ATP, Mg2+, SAM Mg2+ Mg2+ (SAM)

DNA cleavage

requirements

Two recognition

sites in any

orientation

Single recognition

site

Two recognition

sites in a

head-to-head

orientation



Enzymatic

turnover

No Yes Yes

DNA translocation Yes No No

Site of methylation At recognition site At recognition site At recognition site

Table 2-1.4: Comparative properties of restriction enzymes

Fig 2-1.4.3: Cleaving a DNA sequence by a restriction enzyme creates a specific pattern .

Cleaving a single piece of DNA with multiple restriction enzymes creates a "DNA

fingerprint." The pattern of fragments can be compared to similar DNA from another

source treated with the same enzymes, to determine if the two are identical or different.



2-1.5 Cleavage Patterns of Some Common Restriction Endonucleases:

The recognition and cleavage sites and cleavage patterns of HindIII, SmaI, EcoRI,

and BamHI are shown. Cleavage by an endonuclease creates DNA sequence with either a

sticky end or blunt end. The blunt ended fragments can be joined to any other DNA

fragment with blunt ends using linkers/adapters, making these enzymes useful for certain

types of DNA cloning experiments.

Fig 2-1.5: Cleavage patterns of HindIII, SmaI, EcoRI and BamHI



2-1.6 Applications:

In various applications related to genetic engineering DNA is cleaved by using these

restriction enzymes.

• They are used in the process of insertion of genes into plasmid vectors during

gene cloning and protein expression experiments.

• Restriction enzymes can also be used to distinguish gene alleles by specifically

recognizing single base changes in DNA known as single nucleotide

polymorphisms (SNPs). This is only possible if a mutation alters the restriction

site present in the allele.

• Restriction enzymes are used for Restriction Fragment Length Polymorphism

(RFLP) analysis for identifying individuals or strains of a particular species.

Bibliography:

• Lodge J. 2007. Gene cloning: principles and applications. Taylor & Francis

Group.

• Primrose S. B., Twyman R. M., and Old R. W. 2001. Principles of Gene

Manipulation; Oxford: Blackwell Scientific.

• Reece R. J. 2000. Analysis of Genes and Genomes; John Wiley & Sons, U.K.



MODULE 2- LECTURE 2

ENZYMES IN MODIFICATION- POLYNUCLEOTIDE

PHOSPHORYLASE, DNASE AND THEIR MECHANISM

OF ACTION 2-2.1 Polynucleotide phosphorylase:

• Polynucleotide phosphorylase was first discovered from extracts of Azotobacter

agile by Grunberg-Manago and Ochoa.

• Polynucleotide phosphorylase (PNPase) catalyzes the synthesis of long chain

polyribonucleotides (RNA) in 5’ to 3’ direction from nucleotide diphosphates as

precursors and reversibly catalyzes phosphorolytic cleavage of

polyribonucleotides in 3’ to 5’ direction with a release of orthophosphate in

presence of inorganic phosphate.

• PNPase is a bifunctional enzyme and functions in mRNA processing and

degradation inside the cell.

• Structural and physiochemical studies in enzymes showed that it is formed of

subunits. The arrangements of the subunits may vary from species to species

which would alter their properties.

• These enzyme can catalyze not only the synthesis of RNA from the mixtures of

naturally occurring ribonucleoside diphosphates, but also that of non-naturally

occurring polyribonucleotides



2-2.1.1 Mechanism of action: As mentioned earlier, polynucleotide phosphorylase is a bifunctional enzyme. The

mechanism of action of this enzyme can be represented by following reactions:

Fig 2-2.1: Schematic representation of the role of PNPase in poly(A) tail metabolism in E. coli.

(Source: Mohanty B K, and Kushner S R PNAS 2000; 97:11966-11971, copyright

2000, National Academy of Science)

In E.coli, polynucleotide phosphorylase regulates mRNA processing either by

adding ribonucleotides to the 3’ end or by cleaving bases in 3’ to 5’ direction. The

function of PNPase depends upon inorganic phosphate (Pi) concentration inside the cell.

The transcripts are polyadenylated using enzyme polyadenylate polymerase I (PAPI).

After primary polyadenylylation of the transcript by PAP I, PNPase may bind to the 3′

end of the poly(A) tail. PNPase works either degradatively or biosynthetically inside the

cell depending on the Pi concentration. Under high Pi concentration, it degrades the

poly(A) tail releasing adenine diphosphates. If the Pi concentration is low, PAP I



initiates addition of one or more nucleotides to the existing poly (A) tail and in the

process generates inorganic phosphate. On dissociation of PNPase, the 3′ end again is

available to PAP I for further polymerization.

2-2.1.2 Function: Different functions of Polynucleotide phosphorylase are:

• It is involved in mRNA processing and degradation in bacteria, plants, and in

humans.

• It synthesizes long, highly heteropolymeric tails in vivo as well as accounts for all

of the observed residual polyadenylation in poly(A) polymerase I deficient

strains.

• PNPase function as a part of RNA degradosome in E.coli cell. RNA

degradosome is a multicomponent enzyme complex that includes RNaseE

(endoribinuclease), polynucleotide phosphorylase (3’ to 5’ exonuclease), RhlB

helicase (a DEAD box helicase) and a glycolytic enzyme enolase. This complex

catalyzes 3’ to 5’ exonuclease activity in presence of ATP. In eukaryotes, the

exosomes are located in nucleus and cytoplasm. Degradsomes in bacteria and

exosomes in eukaryotes are associated with processing, control and turnover of

RNA transcripts.

• In rDNA cloning technology, it has been used to synthesize radiolabelled

polyribonucleotides from nucleoside diphosphate monomers.

2-2.2 Deoxyribonuclease (DNase):

• A nuclease enzyme that can catalyze the hydrolytic cleavage of phosphodiester

bonds in the DNA backbone are known as deoxyribonuclease (DNase).

• Based on the position of action, these enzymes are broadly classified as

endodeoxyribonuclease (cleave DNA sequence internally) and

exodeoxyribonuclease (cleave the terminal nucleotides).



• Unlike restriction enzymes, DNase does not have any specific

recognition/restriction site and cleave DNA sequence at random locations.

• There is a wide variety of deoxyribonucleases known which have different

substrate specificities, chemical mechanisms, and biological functions. They are:

1) Deoxyribonuclease I (DNaseI):

An endonuclease which cleaves double-stranded DNA or single stranded DNA.

The cleavage preferentially occurs adjacent to pyrimidine (C or T) residues. The major

products are 5'-phosphorylated bi-, tri- and tetranucleotides. It requires divalent ions

(Ca2+ and Mn2+/Mg2+) for its activity and creates blunt ends or 1-2 overhang sequences.

DNaseI is the most widely used enzyme in cloning experiments to remove DNA

contamination from mRNA preparation (to be used for cDNA library preparation,

northern hybridization, RT-PCR etc). The mode of action of DNaseI varies according to

the divalent cation used.

In the presence of magnesium ions (Mg+2), DNaseI hydrolyzes each strand of

duplex DNA producing single stranded nicks in the DNA backbone, generating various

random cleavages.

On the other hand, in the presence of manganese ions (Mn+2), DNaseI cleaves both

strands of a double stranded DNA at approximately the same site, producing blunt ended

DNA fragments or with 1-2 base overhangs. The two major DNases found in metazoans

are: deoxyribonuclease I and deoxyribonuclease II.



Fig 2-2.2 Action of DNase I in the presence of Mg+2 and Mn+2 ions. (Arrowhead denoting random site of cleavage in double

stranded DNA by DNase I)

Some of the common applications of DNase I in rDNA technology have been mentioned

below:

• Eliminating DNA contamination (e.g. plasmid) from preparations of RNA.

• Analyzing the DNA-protein interactions via DNA footprinting.

• Nicking DNA prior to radio-labeling by nick translation.

2) DeoxyribonucleaseII (DNaseII):

It is a non-specific endonuclease with optimal activity at acidic pH (4.5-5.5) and

conserved from human to C.elegans.. It does not require any divalent cation for its

activity. DNaseII initially introduces multiple single stranded nicks in DNA backbone

and finally generates 3’ phosphate groups by hydrolyzing phosphodiester linkages.

This enzyme releases 3’phosphate groups by hydrolyzing phosphodiester linkage

and creating nicks in the DNA backbone. DNaseII acts by generating multiple single

stranded nicks followed by production of acid soluble nucleotides and oligonucleotides.

http://www.vivo.colostate.edu/hbooks/genetics/biotech/manip/labeling.html



The catalytic site of the enzyme contains three histidine residues which are essential for

enzyme activity.

Some of the common applications of DNase II are as follows:

• DNA fragmentation

• Molecular weight marker

• Cell apoptosis assays etc.

3)Exonuclease III:

Exonuclease III is a globular enzyme which has 3’→5’ exonuclease activity in a double

stranded DNA. The template DNA should be double stranded and the enzyme does not

cleave single stranded DNA. The enzyme shows optimal activity with blunt ended

sequences or sequences with 5’ overhang.

Exonuclease III enzyme has a bound divalent cation which is essential for enzyme

activity. The mechanism of the enzyme can be affected by variation in temperature,

monovalent ion concentration in the reaction buffer, and structure and concentration of

3’termini. The enzyme shows optimal activity at 37°C at pH 8.0.

Various application of exonuclease III in molecular cloning experiments are:

• To generate template for DNA sequencing

• To generate substrate for DNA labeling experiments

• Directed mutagenesis

• DNA-protein interaction assays (to find blockage of exonuclease III activity by

protein-DNA binding) etc.



4) Mung bean nuclease:

As the name suggest, this nuclease enzyme is isolated from mung bean sprouts

(Vigna radiata). Mung bean nuclease enzymes can degrade single stranded DNA as well

RNA. Under high enzyme concentration, they can degrade double stranded DNA, RNA

or even DNA/RNA hybrids.

Mung bean nuclease can cleave single stranded DNA or RNA to produce 5’-phosphoryl

mono and oligonucleotides. It requires Zn2+ ion for its activity and shows optimal activity

at 37°C. The enzyme works in low salt concentration (25mM ammonium acetate) and

acidic pH (pH 5.0). Treatment with EDTA or SDS results in irreversible inactivation of

the enzyme.

Mung bean nuclease is less robust than S1 nuclease and easier to handle. It has

been used to create blunt end DNA by cleaving protruding ends from 5’ ends. This

enzyme cannot produce nicks in a double stranded DNA but at higher concentration, it

can generate nicks and cleave double stranded DNA.

Bibliography:

• Boyer P. D. 1981. The Enzymes. Academic press Inc Ltd.

• Heppel L.A., Singer M.F., Hilmoe R.J. 1962. The mechanism of action of

polynucleotide phosphorylase; Annals New York Academy of Sciences.

• http://openi.nlm.nih.gov/detailedresult.php?img=3071783_1423-0127-18-23-

3&req=4

• Mohanty B.K , Kushner S.R. 2000. Polynucleotide phosphorylase functions both

as a 3′ → 5′ exonuclease and a poly(A) polymerase in Escherichia coli;

PNAS;97:11966-11971.

• Singer M.F., Hilmoe R.J. and Manago M.G. 1960. Studies on the mechanism of

action of polynucleotide. J.Bio Chem 236 (9).



MODULE 2-LECTURE-3

ENZYMES IN MODIFICATION- PHOSPHATASES AND METHYLASES AND THEIR MECHANISM OF ACTION

2-3.1 Phosphatase: • Phosphatase catalyses the cleavage of a phosphate (PO4

-2) group from substrate

by using a water molecule (hydrolytic cleavage).

• This reaction is not reversible.

• This shows totally opposite activity from enzyme like kinase and phosphorylase

that add a phosphate group to their substrate. On the basis of their activity there

are two types of phosphatase i.e acid phosphatase and alkaline phosphatase. In

both forms the alkaline phosphatase are most common.

• Special class of phosphatase that remove a phosphate group from protein, called

“Phosphoprotein phosphatase”.

Fig 2-3.1: Schematic representation of hydrolytic cleavage of phosphate group (-PO4

-2).

2-3.1.1 Acid phosphatase:

• It shows its optimal activity at pH between 3 and 6, e.g. a lysosomal enzyme that

hydrolyze organic phosphates liberating one or more phosphate groups. They are

found in prostatic epithelial cells, erythrocyte, prostatic tissue, spleen, kidney etc.

2-3.1.2 Alkaline phosphatase:

• Homodimeric enzyme which catalyzes reactions like hydrolysis and

transphosphophorylation of phosphate monoester.

• They show their optimal activity at pH of about 10.



• Alkaline phosphatase was the first zinc enzyme discovered having three closed

spaced metal ion. Two Zn+2 ions and one Mg+2 ion, in which Zn+2 ions are

bridges by Asp 51. The mechanism of action is based on reaction where a

covalent serine – phosphate intermediate is formed to produce inorganic

phosphate and an alcohol.

• In human body it is present in four isoforms, in which three are tissue specific

isoform i.e. placental, germ cell, intestinal and one is non tissue specific isoform.

The genes that encode for tissue specific isoforms are present on chromosome -2

p37-q37, while the genes for one non tissue specific are present on chromosome -

1 p34- p36.1.

• During post-translational modification, alkaline phosphatase is modified by N-

glycosylation. It undergoes a modification through which uptake of two Zn+2 ion

and one Mg+2 ion occurs which is important in forming active site of that enzyme.

Alkaline phosphatases are isolated from various sources like microorganisms,

tissue of different organs, connective tissue of invertebrate and vertebrate, and

human body.

Fig 2-3.1.2: Action of alkaline phosphatase

There are several AP that are used in gene manipulation-

• Bacterial alkaline phosphatase (BAP) - Bacterial alkaline phosphate is a

phosphomonoester that hydrolyzes 3’ and 5’ phosphate from nucleic acid (DNA/

RNA). It more suitably removes phosphate group before end labeling and

remove phosphate from vector prior to insert ligation. BAP generally shows

optimum activity at temperature 65°C. BAP is sensitive to inorganic phosphate

so in presence of inorganic phosphates activity may reduce.



• Calf intestinal alkaline phosphatase (CIP) – It is isolated from calf intestine,

which catalyzes the removal of phosphate group from 5’ end of DNA as well as

RNA. This enzyme is highly used in gene cloning experiments, as to make a

construct that could not undergo self-ligation. Hence after the treatment with

CIP, without having a phosphate group at 5’ ends a vector cannot self ligate and

recircularise. This step improves the efficiency of vector containing desired

insert.

• Shrimp alkaline phosphatase (SAP) - Shrimp alkaline phosphatase is highly

specific, heat labile phosphatase enzyme isolated from arctic shrimp (Pandalus

borealis). It removes 5’ phosphate group from DNA, RNA, dNTPs and proteins.

SAP has similar specificity as CIP but unlike CIP, it can be irreversibly

inactivated by heat treatment at 65°C for 15mins. SAP is used for 5’

dephosphorylation during cloning experiments for various application as follows:

Dephosphorylate 5’-phosphate group of DNA/RNA for subsequent

labeling of the ends.

To prevent self-ligation of the linearized plasmid.

To prepare PCR product for sequencing.

To inactivate remaining dNTPs from PCR product (for downstream

sequencing appication).

Two primary uses for alkaline phosphatase in DNA modification:

• Removing 5’ phosphate from different vector like plasmid, bacteriophage after

treating with restriction enzyme. This treatment prevents self ligation because

unavailability of phosphate group at end. So, this treatment greatly enhances the

ligation of desired insert. During ligation of desired insert, the complementary

ends of the insert and vector will come to proximity of each other (only for sticky

ends but not for blunt ends). One strand of the insert having 5’-phosphate will

ligate with the 3’OH of the vector and the remaining strand will have a nick. This

nick will be sealed in the next step by ligase enzyme in the presence of ATP. It is

used to remove 5’ phosphate from fragment of DNA prior to labeling with

radioactive phosphate.



2-3.2 Methylase:

• Methyltransferase or methylase catalyzes the transfer of methyl group (-CH3) to

its substrate. The process of transfer of methyl group to its substrate is called

methylation.

• Methylation is a common phenomenon in DNA and protein structure.

• Methyltransferase uses a reactive methyl group that is bound to sulfur in S-

adenosyl methionine (SAM) which acts as the methyl donor.

• Methylation normally occurs on cytosine (C) residue in DNA sequence. In

protein, methylation occurs on nitrogen atom either on N-terminus or on the side

chain of protein.

• DNA methylation regulates gene or silence gene without changing DNA

sequences, as a part of epigenetic regulation.

• In bacterial system, methylation plays a major role in preventing their genome

from degradation by restriction enzymes. It is a part of restriction – modification

system in bacteria.

Methyltransferase can be classified in three groups:

a) m6A-generates N6 methyladenosine,

b) m4C-generates N4 methylcytosine,

c) m5C-generatesN5 methylcytosine.

m6A and m4C methyltransferase are primarily found in prokaryotes. These enzymes are

responsible for methylation of DNA sequences in order to prevent the host from digesting

its own genome via its restriction enzyme.



Fig 2-3.2: Activity of restriction and methylase enzymes

Restriction enzyme EcoRI cleaves within the recognition sequence if the DNA is

unmethylated. On methylation by methylases, the restriction enzyme EcoRI is inhibited

from cleaving within the restriction site.

Some common examples of methytransferases are: DNA adenyl methytransferase

(DAM), histone methyltransferase, O-methyltransferase etc. DAM methylase is generally

used in recombinant DNA technology which can methylate adenine (A) in the sequence

5’GATC3’. This enzyme can methylate a newly synthesized DNA strand on specific

sites.



Bibliography:

• Anderson R. A., Bosron W. F., Kennedy F. S., Vallee B.L. 1975. The role of

magnesium in E.coli alkaline phosphatase. Proc. Natl Acad. Sci. USA, 72: 2989-

2993.

• Gerstein A.S. 2004. Molecular Biology Problem Solver: A Laboratory Guide.

John Wiley & Sons.

• Henthorn P.S., Raducha M., Edwards Y.H., Weiss M.J., Slaughter C., Lafferty

M.A., Harris H. 1987. Nucleotide and amino acid sequences of human intestinal

alkaline phosphatase: close homology to placental alkaline phosphatase. PNAS.

84: 1234-1238.

• Kim E. E., Wyckoff H. W. 1991. Reaction mechanism of alkaline phosphatase

based on crystal structures to metal-ion catalysis. J. Mol. Biol. 218:449-464.

• Knoll B., Rothblum K., Longley M. 1988. Nucleotide sequence of the human

placental alkaline phosphatase gene: Evolution of the 5' flanking region by

deletion/substitution. J. Biol. Chem. 263: 12020-12027.

• Millan, J. L. and Manes, T. 1988. Seminoma-derived Nagao isozyme is encoded

by a germ-cell alkaline phosphatase gene. PNAS. 85: 3024-3028.



MODULE 2-LECTURE 4

ENZYMES IN MODIFICATION- LIGASES,

POLYNUCLEOTIDE KINASE, RNASE AND THEIR

MECHANISM OF ACTION 2-4.1 Ligases:

• DNA ligase catalyses the formation of phosphodiester bond between two

deoxynucleotide residues of two DNA strands.

• DNA ligase enzyme requires a free hydroxyl group at the 3´ -end of one DNA

chain and a phosphate group at the 5´-end of the other and requires energy in the

process.

• E.coli and other bacterial DNA ligase utilizes NAD+ as energy donor, whereas in

T4 bacteriophage, T4 DNA ligase uses ATP as cofactor.

• The role of DNA ligase is to seal nicks in the backbone of double-stranded DNA

after lagging strand formation to join the okazaki fragments.

• This joining process is essential for the normal synthesis of DNA and for

repairing damaged DNA. It has been exploited by genetic engineers to join DNA

chains to form recombinant DNA molecules. Usually single stranded break are

repaired using the complimentary strand as the template but sometimes double

stranded breaks can also be repaired with the help of DNA ligase IV.

• The most widely used DNA ligase is isolated from T4 bacteriophage. T4 DNA

ligase needs ATP as a cofactor. The enzyme from E. coli uses cofactor NAD.

Except this, the catalysis mechanism is somewhat similar for both the ligases. The

role of cofactor is splitting and forming an enzyme-AMP complex which further

aids in formation of phosphodiester bonds between hydroxyl and phosphate

groups by exposing them.



2-4.1.1 Mechanism of Action of DNA Ligases:

• ATP, or NAD+, reacts with the ligase enzyme to form a covalent enzyme–AMP

complex in which the AMP is linked to ε-amino group of a lysine residue in the

active site of the enzyme through a phosphoamide bond.

• The AMP moiety activates the phosphate group at the 5´-end of the DNA

molecule to be joined. It is called as the donor.

• The final step is a nucleophilic attack by the 3´-hydroxyl group on this activated

phosphorus atom which acts as the acceptor. A phosphodiester bond is formed

and AMP is released.

• The reaction is driven by the hydrolysis of the pyrophosphate released during the

formation of the enzyme–adenylate complex. Two high-energy phosphate bonds

are spent in forming a phosphodiester bond in the DNA backbone with ATP

serving as energy source.

• The temperature optimum for T4 DNA ligase mediated ligation in vitro is 16˚C.

However ligation is also achieved by incubation at 4˚C by incubating over night

or at room temperature condition by incubating for 30 minutes.

• Adenylate and DNA-adenylate are the important intermediates of the

phosphodiester bond forming pathway.



Fig 2-4.1.1: The mechanism of DNA joining by DNA ligase.



2-4.1.2 Application:

• DNA ligase enzyme is used by cells to join the “okazaki fragments” during DNA

replication process. In molecular cloning, ligase enzyme has been routinely used

to construct a recombinant DNA. Followings are some of the examples of

application of ligase enzyme in molecular cloning.Joining of adapters and linkers

to blunt end DNA molecule.

• Cloning of restricted DNA to vector to construct recombinant vector.

Fig 2-4.1.2: Ligation of a gene fragment into the vector and transformation of the cell.

2-4.2 Polynucleotide Kinase:

• PNK is a homotetramer with phosphatase activity at 3’ end and kinase activity at

5’ end with a tunnel like active site. The active site has side chains which interact

with NTP donor’s beta-phosphate and 3’ phosphate of acceptor with an acid

which activated 5’ –OH. Lys-15 and Ser-16 are important for the kinase activity

of the enzyme.

• The basic residues of active site of PNK interact with the negatively charged

phosphates of the DNA.

• Polynucleotide kinase (PNK) catalyzes the transfer of a phosphate group (PO4-2)

from γ position of ATP to the 5' end of either DNA or RNA and nucleoside

monophosphate.



• PNK can convert 3' PO4/5' OH ends into 3' PO4/5' PO4 ends which blocks further

ligation by ligase enzyme.

• PNK is used to label the ends of DNA or RNA with radioactive phosphate group.

• T4 polynucleotide kinase is the most widely used PNK in molecular cloning

experiments, which was isolated from T4 bacteriophage infected E.coli.

PNK carries out two types of enzymatic activity:

• Forward reaction: γ-phosphate is transferred from ATP to the 5' end of a

polynucleotide (DNA or RNA). 5’ phosphate is not present either due to chemical

synthesis or dephosphorylation. The 5’ OH nucleophile is activated by

abstraction of the proton. Asp35 of PNK forms the co-ordinate bond with 5’ OH

and attacks γ phosphorus forming an intermediate.

• Exchange reaction: target DNA or RNA having a 5' phosphate is incubated with

an excess of ADP - where PNK transfers the phosphate from the nucleic acid to

an ADP, forming ATP. PNK then performs a forward reaction and transfer a

phosphate from ATP to the target nucleic acid. Exchange reaction is used to label

with radioactive phosphate group.

Fig 2-4.2: Polynucleotide kinase reaction (A) forward (B) exchange.

(Adapted from http://www.vivo.colostate.edu/hbooks/genetics/biotech/)



Fig. 2-4.2.1: Conversion of 5’ dephospho-(deoxy) ribonucleic acid to 5’ phospho-(deoxy) ribonucleic acid by the action of PNK.

The efficiency of phosphorylation is less in exchange reaction compared to

forward reaction. Along with the phosphorylating activity, PNK also has 3' phosphatase

activity.

There are two major uses of PNK:

• The linkers and adopters are phosphorylated along with the fragments of DNA

before ligation, which requires a 5' phosphate. This includes products of

polymerase chain reaction, which are generated by using non-phosphorylated

primers.

• PNK is also used for radio labelling oligonucleotides, generally with 32P for

preparing hybridization probes.

http://www.vivo.colostate.edu/hbooks/genetics/biotech/pcr/index.html



PNK is inhibited by ammonium ions, so ammonium acetate cannot be used to precipitate

nucleic acids before phosphorylation. Sometimes phosphate ions or NaCl of greater than

50 mM concentration can also inhibit this enzyme.

2-4.3 Ribonuclease (RNase):

• Nuclease that can catalyze hydrolysis of ribonucleotides from either single

stranded or double stranded RNA sequence are called ribonucleotides (RNase).

• RNase are classified into two types depending on position of cleavage, i.e.

endoribonuclease (cleave internal bond) and exoribonuclease (cleave terminal

bond).

• RNase is important for RNA maturation and processing.

• RNaseA and RNaseH play important role in initial defence mechanism against

RNA viral infection.

Two common types of ribonucleases are discussed below:

2-4.3.1 RibonucleaseA (RNaseA):

• An endo-ribonuclease that cleaves specifically single-stranded RNA at the 3' end

of pyrimidine residues.

• The RNA is degraded into 3'-phosphorylated mononucleotides C and U residues

and oligonucleotides in the form of 2', 3'-cyclic monophosphate intermediates.

• Optimal temperature for RNaseA is 60˚C (activity range 15-70˚C) and optimal

pH is 7.6.

• RNaseA has two histidine residues in its active site (His12 and His119). In the

first step, His12 acts as a base; accepting proton forming a nucleophile which

then attacks positively charged phosphorus atom. His119 acts as an acid in this

case, donating a proton to oxygenated P-O-R’ bond. The imidazole side chain

acts as base in His 12 here.

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http://www.vivo.colostate.edu/hbooks/genetics/biotech/manip/conc.html



• The side chain of Lys41 and Phe120 further stabilize the transition state.

Nitrogen of the main chain of Phe120 donates hydrogen, thus bonding with the

unbound oxygen atom.

• In the second step the acid base activities get reversed and His119 accepts proton

from water causing hydroxyl attack on cyclic intermediate.

• Activity of RNaseA can be inhibited by alkylation of His12 and His119 residue

essential for activity of the enzyme.

Fig. 2-4.3.1: Mechanism of action of RNase A

Application:

• It is used to remove RNA contamination from DNA sample.

A)



2-4.3.2 RibonucleaseH:

• Non-specific endoribonuclease that degrades RNA by hydrolytic mechanism from

DNA/RNA duplex resulting in single stranded DNA.

• Enzyme bound divalent metal ion is a cofactor here. The product formed is 5’

phosphorylated ssDNA.

• During cDNA library preparation from RNA sample, RNaseH enzyme is used to

cleave RNA strand of DNA-RNA duplex.

Fig 2-4.3.2: Schematic representation of cDNA preparation from mRNA

Bibliography:

• Boyer P. D. 1981. The Enzymes. Academic press Inc Ltd.

• Gerstein A.S. 2004. Molecular Biology Problem Solver: A Laboratory Guide.

John Wiley & Sons.

• Gilbert S. F. 2010. Developmental Biology (9th edition); Sinauer Associates, Inc

module 2: lecture 1 enzymes in genetic engineering

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